2022 06 16/docs patch (#99)

docs/installation.rst

@@ -18,12 +18,20 @@ you have not already. Users can install MIDAS2 and its dependencies with conda p
   conda install -c zhaoc1 -c anaconda -c bioconda -c conda-forge -c defaults midas2
 
 
+If this installation takes a long time to solve dependencies conflicts, we suggest
+following the conda install from YAML file approach in the next section.
+
+
 From Source
 ++++++++++++
 
 Alternatively, users who want the most up-to-date version of the MIDAS code
 can install from source (dependencies installed with Conda).
 
+On a Linux machins, download a copy of MIDAS2 from our GitHub repository,
+and install the dependencies.
+We do not currently support non-Linux environments.
+
 .. code-block:: shell
 
   $ git clone https://github.com/czbiohub/MIDAS2.git
@@ -33,7 +41,7 @@ can install from source (dependencies installed with Conda).
   $ conda activate midas2
   $ cpanm Bio::SearchIO::hmmer --force # Temporary fix for Prokka
 
-  $ pip install midas2
+  $ pip install .
 
 
 .. tip::

docs/quickstart.rst

@@ -8,25 +8,27 @@ Setup
 Install MIDAS2
 -----------------
 
-On a Linux machine, download a copy of MIDAS2 from our GitHub repository, and
-install the dependencies. We do not currently support non-Linux environments.
+The fastest way to install all the dependencies MIDAS2 needed is install from
+YAML file (``midas2.yaml``) using Conda.
 
+On a Linux machine, download a copy of the test data from our GitHub repository release.
 
-..
-    Confirmed that this is the best install method? Seems like the most complicated one...
-    I guess part of the goal here is to get all of the test reads which are saved to
-    github...
+.. code-block:: shell
 
+  $ wget https://github.com/czbiohub/MIDAS2/releases/download/v1.0.0/tests.tar.gz
+  $ tar -zxf tests.tar.gz
+  $ cd tests
 
-.. code-block:: shell
 
-  $ git clone https://github.com/czbiohub/MIDAS2.git
-  $ cd MIDAS2
+Install the dependencies.
+
+.. code-block:: shell
 
   $ conda env create -n midas2 -f midas2.yml
   $ conda activate midas2
   $ cpanm Bio::SearchIO::hmmer --force # Temporary fix for Prokka
 
+
 Install MIDAS2.
 
 .. code-block:: shell
@@ -42,9 +44,9 @@ Alternative installation procedures are also :ref:`described elsewhere<installat
 Example Data
 ------------
 
-Assuming you're in the ``MIDAS2.0/`` directory you just ``cd``-ed to,
-two single-end gzipped FASTQ files are in the folder ``tests/reads``.
-Navigate to the ``tests`` directory ::
+Assuming you're in the ``tests/`` directory you just ``cd``-ed to,
+two single-end gzipped FASTQ files are in the folder ``tests/reads``. If not,
+navigate to the ``tests`` directory ::
 
   $ cd tests
 
@@ -67,6 +69,7 @@ to a new subfolder called ``my_midasdb_uhgg`` ::
 
   $ midas2 database --init --midasdb_name uhgg --midasdb_dir my_midasdb_uhgg
 
+
 ..
     TODO: If I'm not mistaken, this will install the MIDASDB to MIDAS2.0/tests/my_midasdb_uhgg
     Seems like a mistake, since users will run the quickstart and then have to _redo_ the